Wald Tests

Ectoderm (gd7) vs Mesoderm (Toll10b)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 3626

## 
##    N   U1   U2   U3   D3   D2   D1 
## 6029 1157  456  264  244  436 1069

Neuroectoderm (Tollrm9rm10) vs Mesoderm (Toll10b)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 2746

## 
##    N   U1   U2   U3   D3   D2   D1 
## 6909  742  434  270  242  282  776

Neuroectoderm (Tollrm9rm10) vs Ectoderm (gd7)

Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):

## [1] 1193

## 
##    N   U1   U2   U3   D3   D2   D1 
## 8487  369  151  119   94  126  334

Likelihood Ratio Test

Number of significant genes (padj < 0.1):

## [1] 4173

Session Info

## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] EnhancedVolcano_1.8.0       ggrepel_0.9.1              
##  [3] dplyr_1.0.5                 limma_3.46.0               
##  [5] geneplotter_1.68.0          annotate_1.68.0            
##  [7] XML_3.99-0.6                reshape_0.8.8              
##  [9] lattice_0.20-41             ggplot2_3.3.3              
## [11] gridExtra_2.3               biomaRt_2.46.3             
## [13] gplots_3.1.1                RColorBrewer_1.1-2         
## [15] GenomicFeatures_1.42.3      AnnotationDbi_1.52.0       
## [17] knitr_1.31                  DESeq2_1.30.1              
## [19] SummarizedExperiment_1.20.0 Biobase_2.50.0             
## [21] MatrixGenerics_1.2.1        matrixStats_0.58.0         
## [23] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
## [25] IRanges_2.24.1              S4Vectors_0.28.1           
## [27] BiocGenerics_0.36.0        
## 
## loaded via a namespace (and not attached):
##  [1] ggbeeswarm_0.6.0         colorspace_2.0-0         ellipsis_0.3.1          
##  [4] rprojroot_2.0.2          XVector_0.30.0           farver_2.1.0            
##  [7] bit64_4.0.5              fansi_0.4.2              xml2_1.3.2              
## [10] splines_4.0.5            extrafont_0.17           cachem_1.0.4            
## [13] jsonlite_1.7.2           Rsamtools_2.6.0          Rttf2pt1_1.3.8          
## [16] dbplyr_2.1.1             compiler_4.0.5           httr_1.4.2              
## [19] assertthat_0.2.1         Matrix_1.3-2             fastmap_1.1.0           
## [22] htmltools_0.5.1.1        prettyunits_1.1.1        tools_4.0.5             
## [25] gtable_0.3.0             glue_1.4.2               GenomeInfoDbData_1.2.4  
## [28] maps_3.3.0               rappdirs_0.3.3           Rcpp_1.0.6              
## [31] jquerylib_0.1.3          vctrs_0.3.7              Biostrings_2.58.0       
## [34] ggalt_0.4.0              rtracklayer_1.50.0       extrafontdb_1.0         
## [37] xfun_0.22                stringr_1.4.0            lifecycle_1.0.0         
## [40] gtools_3.8.2             zlibbioc_1.36.0          MASS_7.3-53.1           
## [43] scales_1.1.1             hms_1.0.0                proj4_1.0-10.1          
## [46] yaml_2.2.1               curl_4.3                 memoise_2.0.0           
## [49] ggrastr_0.2.3            sass_0.3.1               stringi_1.5.3           
## [52] RSQLite_2.2.6            highr_0.8                genefilter_1.72.1       
## [55] caTools_1.18.2           BiocParallel_1.24.1      rlang_0.4.10            
## [58] pkgconfig_2.0.3          bitops_1.0-6             evaluate_0.14           
## [61] purrr_0.3.4              labeling_0.4.2           GenomicAlignments_1.26.0
## [64] bit_4.0.4                tidyselect_1.1.0         plyr_1.8.6              
## [67] magrittr_2.0.1           R6_2.5.0                 generics_0.1.0          
## [70] DelayedArray_0.16.3      DBI_1.1.1                pillar_1.6.0            
## [73] withr_2.4.1              survival_3.2-10          RCurl_1.98-1.3          
## [76] ash_1.0-15               tibble_3.1.0             crayon_1.4.1            
## [79] KernSmooth_2.23-18       utf8_1.2.1               BiocFileCache_1.14.0    
## [82] rmarkdown_2.7            progress_1.2.2           locfit_1.5-9.4          
## [85] blob_1.2.1               digest_0.6.27            xtable_1.8-4            
## [88] openssl_1.4.3            munsell_0.5.0            beeswarm_0.3.1          
## [91] vipor_0.4.5              bslib_0.2.4              askpass_1.1